1
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Hirohata K, Yamaguchi Y, Maruno T, Shibuya R, Torisu T, Onishi T, Chono H, Mineno J, Yuzhe Y, Higashiyama K, Masumi-Koizumi K, Uchida K, Yamamoto T, Uchida E, Okada T, Uchiyama S. Applications and Limitations of Equilibrium Density Gradient Analytical Ultracentrifugation for the Quantitative Characterization of Adeno-Associated Virus Vectors. Anal Chem 2024; 96:642-651. [PMID: 38165078 PMCID: PMC10794998 DOI: 10.1021/acs.analchem.3c01955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Adeno-associated virus (AAV) vectors are produced as a mixture of the desired particle (full particle, FP), which is filled with the designed DNA, product-related impurities such as particle without DNA (empty particle, EP), and aggregates. Cesium chloride or iodixanol equilibrium density gradient ultracentrifugation (DGE-UC) has been used for the purification of AAV vectors. DGE-UC can separate FP from impurities based on the difference in their buoyant densities. Here, we report the applications and limitations of equilibrium density gradient analytical ultracentrifugation (DGE-AUC) using a modern AUC instrument that employs DGE-UC principles for the characterization and quantitation of AAV vectors. We evaluated the quantitative ability of DGE-AUC in comparison with sedimentation velocity AUC (SV-AUC) or band sedimentation AUC (BS-AUC) using AAVs with different DNA lengths and different serotypes. DGE-AUC enabled the accurate quantification of the ratio of FP to EP when the AAV vector primarily contains these particles. Furthermore, we developed a new workflow to identify the components of separated peaks in addition to FP and EP. Ultraviolet absorption spectra obtained by multiwavelength detection can also support peak assignment following component identification. DGE-AUC experiments for AAV vectors have limitations with regard to minor components with low absorption at the detected wavelength or those with a density similar to that of major components of AAV vectors. DGE-AUC is the only analytical method that can evaluate particle density heterogeneity; therefore, SV-AUC or BS-AUC and DGE-AUC are complementary methods for reliable assessment of the purity of AAV vectors.
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Affiliation(s)
- Kiichi Hirohata
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Yamaguchi
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Maruno
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Risa Shibuya
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Torisu
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takayuki Onishi
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideto Chono
- Takara
Bio Inc., 7-4-38 Nojihigashi, Kusatsu, Shiga 525-0058, Japan
| | - Junichi Mineno
- Takara
Bio Inc., 7-4-38 Nojihigashi, Kusatsu, Shiga 525-0058, Japan
| | - Yuan Yuzhe
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kiyoko Higashiyama
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kyoko Masumi-Koizumi
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kazuhisa Uchida
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takenori Yamamoto
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-city, Kanagawa 210-9501, Japan
| | - Eriko Uchida
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-city, Kanagawa 210-9501, Japan
| | - Takashi Okada
- Institute
of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Susumu Uchiyama
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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2
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Nishio T, Masaoka T, Yoshikawa Y, Sadakane K, Kenmotsu T, Schiessel H, Yoshikawa K. Markedly Different Effects of Monovalent Cations on the Efficiency of Gene Expression. Adv Biol (Weinh) 2023; 7:e2200164. [PMID: 36328593 DOI: 10.1002/adbi.202200164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/20/2022] [Indexed: 11/06/2022]
Abstract
The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system is examined using a luciferase assay. It is found that the potency for all ions analyzed here is in the order Rb+ > K+ > Cs+ > Na+ ≈ Li+ > (CH3 )4 N+ , where Rb+ is most efficient at promoting TX-TL and the ions of Li+ , Na+ , and (CH3 )4 N+ exhibit an inhibitory effect. Similar promotion/inhibition effects are observed for cell-free TL alone with an mRNA template.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Tomoya Masaoka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics Institute for Advanced Study, Kyoto University, Kyoto, 606-8501, Japan
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3
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Sun LZ, Qian JL, Cai P, Xu X. Mutual effects between single-stranded DNA conformation and Na +-Mg 2+ ion competition in mixed salt solutions. Phys Chem Chem Phys 2022; 24:20867-20881. [PMID: 36043348 DOI: 10.1039/d2cp02737b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted growing attention because of its biological and technological importance. Although single-species ion effects have been extensively explored, it is challenging to study the ssDNA conformational properties under mixed monovalent/divalent ion conditions due to the complications of ssDNA flexibility and ion-ion competition. In this study, we apply Langevin dynamics simulations to investigate mixed Na+/Mg2+ ion-dependent ssDNA conformations. The ssDNA structure is described using a coarse-grained model, in which the phosphate, base, and sugar of each nucleotide are represented by three different beads. A novel improvement in our simulation model is that mixed-salt-related electrostatic interactions are computed via combining Manning counterion condensation (MCC) theory with the Monte Carlo tightly bound ion (MCTBI) model. Based on this MCC-MCTBI combination, we report new empirical functions to describe the ion-concentration-dependent and ssDNA conformation/structure-dependent electrostatic effects. The calculation results relating to the ion binding properties and the simulation results relating to the ssDNA conformational properties are validated against experimental results. In addition, our simulation results suggest a quantitative relationship between the ssDNA conformation and Na+-Mg2+ competition; this in turn reveals their mutual impact in the ion atmosphere.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Jun-Lin Qian
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Pinggen Cai
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, 213001, China
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4
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Chalikian TV, Macgregor RB. Volumetric Properties of Four-Stranded DNA Structures. BIOLOGY 2021; 10:813. [PMID: 34440045 PMCID: PMC8389613 DOI: 10.3390/biology10080813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022]
Abstract
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute-solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.
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Affiliation(s)
- Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada;
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5
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Vo TD, Schneider AL, Wilson WD, Poon GMK. Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6. Phys Chem Chem Phys 2021; 23:13490-13502. [PMID: 34120158 PMCID: PMC8233815 DOI: 10.1039/d1cp01568k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to interfacial ion pairs with DNA. The role of extra-interfacial ionic interactions, particularly as dynamic drivers of DNA sequence selectivity, remain poorly known. The ETS family of transcription factors represents an attractive model for addressing this knowledge gap given their diverse ionic composition in primary structures that fold to a tightly conserved DNA-binding motif. To probe the importance of extra-interfacial salt bridges in DNA recognition, we compared the salt-dependent binding by Elk1 with ETV6, two ETS homologs differing markedly in ionic composition. While both proteins exhibit salt-dependent binding with cognate DNA that corresponds to interfacial phosphate contacts, their nonspecific binding diverges from cognate binding as well as each other. Molecular dynamics simulations in explicit solvent, which generated ionic interactions in agreement with the experimental binding data, revealed distinct salt-bridge dynamics in the nonspecific complexes formed by the two proteins. Impaired DNA contact by ETV6 resulted in fewer backbone contacts in the nonspecific complex, while Elk1 exhibited a redistribution of extra-interfacial salt bridges via residues that are non-conserved between the two ETS relatives. Thus, primary structure variation in ionic residues can encode highly differentiated specificity mechanisms in a highly conserved DNA-binding motif.
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Affiliation(s)
- Tam D Vo
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
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6
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Liu L, Kim BG, Feroze U, Macgregor RB, Chalikian TV. Probing the Ionic Atmosphere and Hydration of the c-MYC i-Motif. J Am Chem Soc 2018; 140:2229-2238. [DOI: 10.1021/jacs.7b11537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Ujala Feroze
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B. Macgregor
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
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7
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Rubio AR, Busto N, Leal JM, García B. Doxorubicin binds to duplex RNA with higher affinity than ctDNA and favours the isothermal denaturation of triplex RNA. RSC Adv 2016. [DOI: 10.1039/c6ra21387a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The higher affinity of DOX with AU to give the intercalated complex AU/DOX is responsible for the disproportionation of the groove binding complex, UAU/DOX, to give rise to the AU/DOX and the U/DOX complexes at 25 °C
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Affiliation(s)
- Ana R. Rubio
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - Natalia Busto
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - José M. Leal
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
| | - Begoña García
- Chemistry Department
- University of Burgos
- 09001 Burgos
- Spain
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8
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Ruiz R, Hoyuelos FJ, Navarro AM, Leal JM, García B. Unequal effect of ethanol-water on the stability of ct-DNA, poly[(dA-dT)]₂ and poly(rA)·poly(rU). Thermophysical properties. Phys Chem Chem Phys 2014; 17:2025-33. [PMID: 25477190 DOI: 10.1039/c4cp03459g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethanol affects unequally the thermal stability of DNA and RNA. It stabilizes RNA, while destabilizing DNA. The variation of the relative viscosity (η/η0) of [poly(dA-dT)]2 with temperature unveils transitions close to the respective denaturation temperature, calculated spectrophotometrically and calorimetrically. From the raw data densities and speeds of sound, the volumetric observables were calculated. In all cases studied, a change in sign from low to high ethanol content occurred for both partial molar volume (ϕV) and partial molar adiabatic compressibility (ϕK(S)). The minima, close to 10%, should correspond to the highest solvation and the maxima, close to 30%, to the lowest solvation. For 40-50% ethanol, the solvation increases again. The complex structure of ethanol-water, for which changes are observed in regions close to such critical concentrations, justifies the observed behaviour. The variation of ϕV and ϕK(S) was sharper for RNA compared with respect to DNA, indicating that the solvation sequence is poly(rA)·poly(rU) < ct-DNA < [poly(dA-dT)]2.
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Affiliation(s)
- Rebeca Ruiz
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain.
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9
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Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Biopolymers 2013; 101:216-27. [DOI: 10.1002/bip.22317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Yuen Lai Shek
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Golamreza Dehghan Noudeh
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Mozhgan Nazari
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Heiko Heerklotz
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Rashid M. Abu-Ghazalah
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - David N. Dubins
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
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10
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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11
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Amiri AR, Macgregor RB. The effect of hydrostatic pressure on the thermal stability of DNA hairpins. Biophys Chem 2011; 156:88-95. [DOI: 10.1016/j.bpc.2011.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 02/02/2011] [Accepted: 02/08/2011] [Indexed: 11/29/2022]
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12
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Fan HY, Shek YL, Amiri A, Dubins DN, Heerklotz H, Macgregor RB, Chalikian TV. Volumetric characterization of sodium-induced G-quadruplex formation. J Am Chem Soc 2011; 133:4518-26. [PMID: 21370889 DOI: 10.1021/ja110495c] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oligodeoxyribonucleotides (ODN) with repeats of the human telomeric sequence can adopt different tetrahelical conformations that exhibit similar energetic parameters. We studied the volumetric properties of the folded and unfolded states of an ODN with four repeats of the human telomeric sequence, d[A(GGGTTA)(3)GGG], by combining pressure-perturbation calorimetry (PPC), vibrating tube densimetry, ultrasonic velocimetry, and UV melting under high pressure. We carried out our volumetric measurements in aqueous buffers at pH 7 containing 20, 50, and 100 mM NaCl. All of the methods employed yielded volumetric parameters that were in excellent agreement. The molar volume changes, ΔV, of the conformational transition leading to formation of the folded state are large and positive. At 50 mM NaCl, the average transition volume, ΔV(tr), obtained from all the methods is 56.4 ± 3.5 cm(3) mol(-1) at the transition temperature of 47 °C, with ΔV(tr) decreasing with an increase in temperature. We carried out a molecular dynamics simulation of the change in the intrinsic geometric parameters of the ODN accompanying quadruplex formation. On the basis of the experimental and computational results, the folding transition of the ODN is accompanied by a release of 103 ± 44 water molecules from its hydration shell to the bulk. This number corresponds to ~18% of the net hydration of the coil conformation.
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Affiliation(s)
- Helen Y Fan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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13
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Benda L, Schneider B, Sychrovský V. Calculating the Response of NMR Shielding Tensor σ(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation. J Phys Chem A 2011; 115:2385-95. [DOI: 10.1021/jp1114114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
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14
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Reis JCR, Santos ÂFS, Lampreia IMS. Chemical Thermodynamics of Ultrasound Speed in Solutions and Liquid Mixtures. Chemphyschem 2010; 11:508-16. [DOI: 10.1002/cphc.200900709] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Rayan G, Tsamaloukas AD, Macgregor RB, Heerklotz H. Helix-coil transition of DNA monitored by pressure perturbation calorimetry. J Phys Chem B 2009; 113:1738-42. [PMID: 19159195 DOI: 10.1021/jp808253t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first use of pressure perturbation calorimetry (PPC) to characterize the heat-induced helix-coil transition of DNA polymers. The alternating copolymer poly[d(A-T)] was studied in aqueous solutions containing 5.2 and 18.2 mM Na+; it exhibited helix-coil transition temperatures of 33.6 and 44.7 degrees C, respectively. The transition is accompanied by a negative molar volume change, DeltaV) -2.6 and -2.1 mL/mol (base pair), respectively, and an increase in the coefficient of thermal expansion, Deltaalpha=+5x10(-4) K(-1) (at both ionic strengths). These values are consistent with a greater hydration of the coil form. The larger water-accessible surface area of the coil causes more water molecules to assume a bound, more densely packed structure that then gradually decreases with increasing temperature, leading to a larger value of R. The magnitude of the volume changes detected by PPC were larger than those deduced from high-pressure UV spectroscopy, shedding light on the effect of pressure on DeltaV. The shape of the PPC peak was nearly identical to the shape of the DSC peak, providing direct evidence for the correlation between the molar volume change and enthalpy change for the helix to coil transition of DNA.
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Affiliation(s)
- Gamal Rayan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
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16
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Shi X, Macgregor RB. Effect of cesium on the volume of the helix-coil transition of dA.dT polymers and their ligand complexes. Biophys Chem 2007; 130:93-101. [PMID: 17761381 DOI: 10.1016/j.bpc.2007.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/01/2007] [Accepted: 08/01/2007] [Indexed: 11/18/2022]
Abstract
The pressure dependence of the helix-coil transition of poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)] in aqueous solutions of NaCl and CsCl at concentrations between 10 and 200 mM is reported and used to calculate the accompanying volume change. We also investigated the binding parameters and volume change of ethidium bromide binding with poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)] in aqueous solutions of these two salts. The volume change of helix-coil transition of poly(dA).poly(dT) in Cs(+)-containing solutions differs by less than 1 cm(3) mol(-1) from the value measured when Na(+) is the counter-ion. We propose that this insensitivity towards salt type arises if the counter-ions are essentially fully hydrated around DNA and the DNA conformation is not significantly altered by salt types. Circular dichroism spectroscopy showed that the previously observed large volumetric disparity for the helix-coil transition of poly[d(A-T)].poly[d(A-T)] in solutions containing Na(+) and Cs(+) is likely result of a Cs(+)-induced conformation change that is specific for poly[d(A-T)].poly[d(A-T)]. This cation-specific conformation difference is mostly absent for poly(dA).poly(dT) and EB bound poly[d(A-T)].poly[d(A-T)].
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Affiliation(s)
- Xuesong Shi
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2 Canada
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Shi X, Macgregor RB. The Effect of Charge on the Volume Change of DNA Binding with Intercalator DAPP. J Phys Chem B 2007; 111:3321-4. [PMID: 17388497 DOI: 10.1021/jp068424o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study the effect of ligand charge on DNA-ligand binding, we measured the difference in volume change of the noncovalent complex formed between calf thymus DNA and the charged and uncharged form of 3,8-diamino-6-phenylphenanthridine (DAPP). We found that the volume change for binding with the charged DAPPH+ is about 7.8 +/- 1.5 cm3 mol(-1) more positive than with the neutral DAPP. We hypothesize that this large difference in interaction volume originates from partial desolvation of the charge of DAPPH+ when it is bound to DNA.
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Stellwagen E, Dong Q, Stellwagen NC. Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method. Biochemistry 2007; 46:2050-8. [PMID: 17253778 PMCID: PMC2532990 DOI: 10.1021/bi062132w] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A variation of affinity capillary electrophoresis, called the replacement ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The method was validated by measuring the binding of Li+ ions to adenosine nucleotides; the apparent dissociation constants obtained by the RI method are comparable to literature values obtained by other methods. The binding of Tris+, NH4+, Li+, Na+, and K+ to dsDNA was then investigated. The apparent dissociation constants observed for counterion binding to a random-sequence 26-base pair (bp) oligomer ranged from 71 mM for Tris+ to 173 mM for Na+ and K+. Hence, positively charged Tris buffer ions will compete with other monovalent cations in Tris-buffered solutions. The bound cations identified in this study may correspond to the strongly correlated, tightly bound ions recently postulated to exist as a class of ions near the surface of dsDNA (Tan, Z.-J., and Chen, S.-J. (2006) Biophys. J. 91, 518-536). Monovalent cation binding to random-sequence dsDNA would be expected to occur in addition to any site-specific binding of cations to A-tracts or other DNA sequence motifs. Single-stranded DNA oligomers do not bind the five tested cations under the conditions investigated here.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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Li X, Peng Y, Ren J, Qu X. Carboxyl-modified single-walled carbon nanotubes selectively induce human telomeric i-motif formation. Proc Natl Acad Sci U S A 2006; 103:19658-63. [PMID: 17167055 PMCID: PMC1750900 DOI: 10.1073/pnas.0607245103] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Indexed: 11/18/2022] Open
Abstract
As the leading nanodevice candidate, single-walled carbon nanotubes (SWNTs) have potential therapeutic applications in gene therapy and novel drug delivery. We found that SWNTs can inhibit DNA duplex association and selectively induce human telomeric i-motif DNA formation by binding to the 5'-end major groove under physiological conditions or even at pH 8.0. SWNT binding to telomeric DNA was studied by UV melting, NMR, S1 nuclease cleavage, CD, and competitive FRET methods. These results suggest that SWNTs might have the intriguing potential to modulate human telomeric DNA structures in vivo, like biologically relevant B-A and B-Z DNA transitions, which is of great interest for drug design and cancer therapy.
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Affiliation(s)
- Xi Li
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Yinghua Peng
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jinsong Ren
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaogang Qu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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Ghazaryan AA, Dalyan YB, Haroutiunian SG, Tikhomirova A, Taulier N, Wells JW, Chalikian TV. Thermodynamics of interactions of water-soluble porphyrins with RNA duplexes. J Am Chem Soc 2006; 128:1914-21. [PMID: 16464093 DOI: 10.1021/ja054070n] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We characterized the interactions of meso-tetrakis(4N-(2-hydroxyethyl)pyridinium-4-yl) porphyrin (TEtOHPyP4), meso-tetrakis(4N-allylpyridinium-4-yl) porphyrin (TAlPyP4), and meso-tetrakis(4N-metallylpyridinium-4-yl) porphyrin (TMetAlPyP4) with the poly(rA)poly(rU) and poly(rI)poly(rC) RNA duplexes between 18 and 45 degrees C by employing circular dichroism, light absorption, and fluorescence intensity spectroscopic measurements. Our results suggest that TEtOHPyP4 and TAlPyP4 intercalate into the poly(rA)poly(rU) and poly(rI)poly(rC) host duplexes, while TMetAlPyP4 associates with these RNA duplexes by forming outside-bound, self-stacked aggregates. We used our temperature-dependent absorption titration data to determine the binding constants and stoichiometry for each porphyrin-RNA binding event studied in this work. From the temperature dependences of the binding constants, we calculated the binding free energies, DeltaG(b), enthalpies, DeltaH(b), and entropies, DeltaS(b). For each RNA duplex, the binding enthalpy, DeltaH(b), is the most favorable for TEtOHPyP4 (an intercalator) followed by TAlPyP4 (an intercalator) and TMetAlPyP4 (an outside binder). On the other hand, for each duplex, external self-stacking of TMetAlPyP4 produces the most favorable change in entropy, DeltaS(b), followed by the intercalators TAlPyP4 and TEtOHPyP4. Thus, our results suggest that the thermodynamic profile of porphyrin-RNA binding may correlate with the binding mode. This correlation reflects the differential nature of molecular forces that stabilize/destabilize the two modes of binding-intercalation versus external self-stacking along the host duplex.
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Affiliation(s)
- Ara A Ghazaryan
- Department of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
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Guzman MR, Liquier J, Taillandier E. Hydration and conformational transitions in DNA, RNA, and mixed DNA-RNA triplexes studied by gravimetry and FTIR spectroscopy. J Biomol Struct Dyn 2005; 23:331-9. [PMID: 16218757 DOI: 10.1080/07391102.2005.10507068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have studied by gravimetric measurements and FTIR spectroscopy the hydration of duplexes and triplexes formed by combinations of dA(n), dT(n), rA(n), and rU(n) strands. Results obtained on hydrated films show important differences in their hydration and in the structural transitions which can be induced by varying the water content of the samples. The number of water molecules per nucleotide (w/n) measured at high relative humidity (98% R.H.) is found to be 21 for dA(n).dT(n) and 15 for rA(n).rU(n). Addition of a third rU(n) strand does not change the number of water molecules per nucleotide: w/n=21 for rU(n)*dA(n).dT(n) and w/n=15 for rU(n)*rA(n).rU(n). On the contrary, the addition of a third dT(n) strand changes the water content but in a different way, depending whether the duplex is DNA or RNA. Thus, a loss of four water molecules per nucleotide is measured for dT(n)*dA(n).dT(n) while an increase of two water molecules per nucleotide is observed for dT(n)*rA(n).rU(n). The final hydration is the same for both triplexes (w/n=17). The desorption profiles obtained by gravimetry and FTIR spectroscopy are similar for the rA(n).rU(n) duplex and the rU(n)*rA(n).rU(n) triplex. On the contrary, the desorption profiles of the dA(n).dT(n) duplex and the triplexes formed with it (rU(n)*dA(n).dT(n) and dT(n)*dA(n).dT(n)) are different from each other. This is correlated with conformational transitions induced by varying the hydration content of the different structures, as shown by FTIR spectroscopy. Modifications of the phosphate group hydration and of the sugar conformation (S to N type repuckering) induced by decrease of the water content are observed in the case of triplexes formed on the dA(n).dT(n) duplex.
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Affiliation(s)
- M R Guzman
- Laboratoire BioMoCeTi, UMR CNRS 7033, Universite Paris 13, 74 rue Marcel Cachin, F93017 Bobigny Cedex, France
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Tikhomirova A, Taulier N, Chalikian TV. Energetics of nucleic acid stability: the effect of DeltaCP. J Am Chem Soc 2005; 126:16387-94. [PMID: 15600340 DOI: 10.1021/ja046387d] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report high-resolution differential scanning calorimetric data on the poly(dAdT)poly(dAdT), poly(dA)poly(dT), poly(dIdC)poly(dIdC), poly(dGdC)poly(dGdC), poly(rA)poly(rU), and poly(rI)poly(rC) nucleic acid duplexes. We use these data to evaluate the melting temperatures, TM, enthalpy changes, DeltaHM, and heat capacity changes, DeltaCP, accompanying helix-to-coil transitions of each polymeric duplex studied in this work at different NaCl concentrations. In agreement with previous reports, we have found that DeltaCP exhibits a positive, nonzero value, which, on average, equals 268 +/- 33 J mol(-1) K(-1). With DeltaCP, we have calculated the transition free energies, DeltaG, enthalpies, DeltaH, and entropies, DeltaS, for the duplexes as a function of temperature. Since, DeltaG, DeltaH, and DeltaS all strongly depend on temperature, the thermodynamic comparison between DNA and/or RNA duplexes (that may differ from one another with respect to sequence, composition, conformation, etc.) is physically meaningful only if extrapolated to a common temperature. We have performed such comparative analyses to derive differential thermodynamic parameters of formation of GC versus AT, AU, and IC base pairs as well as B' versus A and B helix conformations. We have proposed some general microscopic interpretations for the observed sequence-specific and conformation-specific thermodynamic differences between the duplexes.
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Affiliation(s)
- Anna Tikhomirova
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada
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